Growth factor receptor network (GFRN) characterization in breast cancer

2(A)-(D): Analysis of pathway activity and intrinsic subtypes

2(A): TCGA BRCA all pathway

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2(B): ICBP all pathways

2(C): TCGA, k-means of 4 pathways

2(D): ICBP, k-means of 4 pathways

3(A)-(C): Unsupervised variance analysis confirms the significance of the GFRN phenotypes

Perform Principal Component Analysis in ICBP cell lines

3(A): Principal Component Analysis in TCGA BRCA

## [1] "Proportion of variance contributed by first 5 principal components in TCGA BRCA gene expression data: 0.343182614266816"

3(B): Boxplot TCGA Principal Components across clinical subtypes (IHC: ER, PR, HER2)

3(C) Correlate TCGA Principal Components with ASSIGN generated GFRN pathway predictions

4(A)-(E):Survival and growth phenotypes express dichotomous cell survival mechanism

4(A):Heatmap of breast cancer cell lines from Western Blot

4(C)-(E): Gene and protein expression are significantly different between growth and survival phenotypes

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## [1] "analyzing BIM"
## [1] "BIM data available"

## [1] "analyzing BAD"
## [1] "BAD data available"

## [1] "analyzing MCL1"

5(A) &(B): Growth factor network phenotypes reflect dichotomous drug response in breast cancer cell lines

5(A): Correlate ICBP GFRN pathway predictions with ICBP drug response and make Heatmap

5(B): Correlate GFRN pathway predictions with drug response in an independent drug assay and make Heatmap

Supplemental Figures 3(A)-(H): Pathway validations codes are in ./ASSIGN folder

Supplemental Figures 4(A)-(G): Boxplot GFRN pathway activity across breast cancer clinical subtypes (IHC)

Supplemental Figures 5(A)-(G): Boxplot GFRN pathway activity across breast cancer intrinsic subtypes (PAM50)

## [1] "517 names have been changed"

##  [1] "AKT"      "BAD"      "EGFR"     "HER2"     "IGF1R"    "KRASG12V"
##  [7] "RAF1"     "Type"     "Siglust"  "PAM50"

Supplemental Figure 6(A)&(B): Boxplot TCGA Principal Components across BRCA intrinsic subtypes (PAM50)

## [1] "Spearman correlation of PC1 and mean gene expression of each sample:  -0.786414519142557"

Supplemental Figures 7(A)-(D):

This analysis was run on Tue Jun 28 12:37:23 2016